I set up a galaxy instance on the cloud, but got the following error
when trying to convert a bed file of hg18 coordinates to fasta
sequence with the "Extract Genomic DNA" tool as a test of the
functionality of this instance:
No sequences are available for 'hg18', request them by reporting this
error.
Where did I go wrong? Likely I would get a similar error for other
databases and indexes I might need and the instructions on the
bitbucket site does not cover this (https://bitbucket.org/galaxy
/galaxy-central/wiki/cloud).
Otherwise this is a very nice setup.
Thomas Randall, PhD
Bioinformatics Scientist, Contractor
National Institute of Environmental Health Sciences
P.O. Box 12233, Research Triangle Park, NC 27709
randallta2@niehs.nih.gov<mailto:randallta2@niehs.nih.gov>
919-541-2271

Hi Thomas,
It turns out you discovered a bug in the cloud setup. We're missing a
2bit
file and a respective reference to the file for the extract genomic
DNA
tool. We'll update the deployment but in the mean time you can
configure the
instance yourself with just a few commands:
# connect to the instance
[local] $ ssh -i <aws private="" key="" file=""> ubuntu@<instance public="" ip="">
# Become galaxy user
[ec2] $ sudo su galaxy
# Change to the data dir and create 2bit file
[ec2] $ cd /mnt/galaxyIndices/genomes/Hsapiens/hg18/seq; faToTwoBit
hg18.fa
hg18.2bit
# Update respective .loc file:
[ec2]: vi /mnt/galaxyTools/galaxy-central/tool-data/alignseq.loc
# add this line at the bottom (use TAB to separate the 3 columns)
seq hg18 /mnt/galaxyIndices/genomes/Hsapiens/hg18/seq/hg18.2bit
That should do it.
Let us know if you have any more trouble and we'll fix this issue when
we
release a new version of the deployment.
Enis
On Fri, Apr 15, 2011 at 11:55 AM, Randall, Thomas (NIH/NIEHS) [C] <